Re: Question about openbabel ECFP fingerprint

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Re: Question about openbabel ECFP fingerprint

Geoffrey Hutchison-3
I am not sure if the current implementation of ECFP supports folding. It was contributed by Noel O'Boyle and NextMove - maybe they can comment.


On Oct 28, 2016, at 3:03 PM, Lirong Wang <[hidden email]> wrote:

Dear Dr. Hutchison,
  How are you? This is Lirong from school of pharmacy and I am an openbabel user. It is exciting the you have implemented the ECFP fingerprint in the latest version of openbabel. I am currently working on a project to index compounds in chembl database with ECFP(4 and 6).  I would like the ECFP fingerprint folded into either 1024 or 2048 bits to speed up the calculation. I used the commandline “babel -ismi test.smi -ofpt -xfECFP6 -xh test_ECFP6.fp”. But it seems not as the FP2 fingerprint(“babel -ismi test.smi -ofpt -xfFP2 -xh test_FP2.fp”). That is the fingerprints of the two compounds seem not the same length in test_ecfp6.fp. I also tried “–xN1024”, but still not the same length. Could you please help me on that? Thanks.
Lirong Wang, PhD
Assistant Professor
Computational Chemical Genomics Screening Center 
Department of Pharmaceutical Sciences/School of Pharmacy 
University of Pittsburgh
528 Salk Hall, 3501 Terrace Street
Pittsburgh, PA 15213

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